Variant report

Variant	rs299479
Chromosome Location	chr12:29709090-29709091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10400534	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10400541	0.95[CEU][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs10492312	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10771550	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771551	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771552	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10843445	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050284	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11050285	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050308	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12372765	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1326758	0.95[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs1409615	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs148898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529908	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159685	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159687	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159689	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159690	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159694	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs159695	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159696	0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs159697	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159698	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159699	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs159700	0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs159713	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs159716	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs177254	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1863224	0.91[JPT][hapmap]
rs2081429	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2113879	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs2113880	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs2162033	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2194819	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2209660	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2209661	0.91[JPT][hapmap]
rs2209662	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2225065	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs2243623	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2254945	0.92[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288131	0.91[CEU][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs2288230	0.86[ASN][1000 genomes]
rs2350532	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs2710775	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2766599	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2766600	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2766601	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2766602	0.95[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2766604	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299444	1.00[CEU][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs299445	1.00[CEU][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs299453	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299454	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299456	0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs299457	0.90[EUR][1000 genomes]
rs299458	0.83[ASN][1000 genomes]
rs299462	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs299463	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs299464	0.91[ASN][1000 genomes]
rs299465	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs299466	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs299467	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299468	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299469	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs299470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299471	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299472	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs299475	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs299487	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366998	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3910440	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3910441	0.87[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4931204	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57231427	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7311193	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7959535	0.91[JPT][hapmap]
rs7960782	0.91[JPT][hapmap]
rs7965227	0.91[JPT][hapmap]
rs994171	0.82[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:29691200-29709200	Weak transcription	HMEC	breast
4	chr12:29698200-29712600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:29699400-29709600	Weak transcription	Left Ventricle	heart
6	chr12:29699400-29715800	Weak transcription	Right Ventricle	heart
7	chr12:29700000-29712000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:29700200-29712200	Weak transcription	Ovary	ovary
9	chr12:29700400-29712000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:29700400-29719000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
12	chr12:29700600-29711400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:29700800-29709600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:29701000-29709400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:29701000-29714200	Weak transcription	HSMMtube	muscle
16	chr12:29701200-29714400	Weak transcription	NHDF-Ad	bronchial
17	chr12:29701200-29714400	Weak transcription	NHLF	lung
18	chr12:29701200-29715200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:29701200-29715600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:29701400-29711600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:29703800-29715200	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:29704000-29709200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:29705000-29711600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:29705000-29716000	Weak transcription	Spleen	Spleen
25	chr12:29706000-29715200	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:29706200-29715000	Weak transcription	Osteobl	bone
27	chr12:29706400-29711600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:29706600-29709400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:29706600-29716200	Weak transcription	Aorta	Aorta
30	chr12:29706800-29711400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:29706800-29712200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:29706800-29712200	Weak transcription	Liver	Liver
33	chr12:29707400-29712200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:29707400-29714600	Weak transcription	Fetal Heart	heart
35	chr12:29707800-29712600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:29708600-29710600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:29708800-29709200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:29708800-29709800	Strong transcription	Adipose Nuclei	Adipose
39	chr12:29708800-29710000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:29708800-29710000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:29708800-29710000	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:29708800-29710200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:29709000-29710000	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr12:29709000-29710000	Strong transcription	Hela-S3	cervix
45	chr12:29709000-29710000	Strong transcription	HSMM	muscle

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